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- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
1YT7|pdb_00001yt7
Cathepsin K complexed with a constrained ketoamide inhibitor
- PDB DOI: https://doi.org/10.2210/pdb1YT7/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2005-02-10 Released: 2005-07-19
- Deposition Author(s): Barrett, D.G.,Boncek, V.M.,Catalano, J.G.,Deaton, D.N.,Hassell, A.M.,Jurgensen, C.H.,Long, S.T.,McFadyen, R.B.,Miller, A.B.,Miller, L.R.,Payne, J.A.,Ray, J.A.,Samano, V.,Shewchuk, L.M.,Tavares, F.X.,Wells-Knecht, K.J.,Willard, D.H.,Wright, L.L.,Zhou, H.Q.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 (Depositor), 0.180 (DCC)
- R-Value Work: 0.183 (Depositor), 0.190 (DCC)
Starting Model:experimental
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Download MendeleyP(2)-P(3) conformationally constrained ketoamide-based inhibitors of cathepsin K.
Barrett, D.G., Boncek, V.M., Catalano, J.G., Deaton, D.N., Hassell, A.M., Jurgensen, C.H., Long, S.T., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Ray, J.A., Samano, V., Shewchuk, L.M., Tavares, F.X., Wells-Knecht, K.J., Willard, D.H., Wright, L.L., Zhou, H.Q.(2005) Bioorg Med Chem Lett 15: 3540-3546
- PubMed: 15982880 Search on PubMed
- DOI: https://doi.org/10.1016/j.bmcl.2005.05.062
- Primary Citation of Related Structures:
1YT7 - PubMed Abstract:
An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker and modifications to P(1') elements led to an enhancement in potency, solubility, clearance, and bioavailability. These optimized inhibitors attenuated bone resorption in a rat TPTX hypocalcemic bone resorption model.
Organizational Affiliation:
Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (3FC)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 24.3 kDa
- Atom Count: 1,790
- Modelled Residue Count: 214
- Deposited Residue Count: 215
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cathepsin K | 215 | Homo sapiens | Mutation(s): 0 Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P43235 (Homo sapiens) Explore P43235 Go to UniProtKB: P43235 | |||||
PHAROS: P43235 GTEx: ENSG00000143387 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 3FC Query on 3FC Download Ideal Coordinates CCD File | D [auth A] | (1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE C26 H32 F3 N5 O7 IXXKXSFSQVTOKQ-ZWKOTPCHSA-N |  | ||
| SO4 Query on SO4 Download Ideal Coordinates CCD File | B [auth A], C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 (Depositor), 0.180 (DCC)
- R-Value Work: 0.183 (Depositor), 0.190 (DCC)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.645 | α = 90 |
| b = 65.645 | β = 90 |
| c = 34.467 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | refinement |
| CNS | phasing |
Deposition Data
- Released Date: 2005-07-19 Deposition Author(s): Barrett, D.G.,Boncek, V.M.,Catalano, J.G.,Deaton, D.N.,Hassell, A.M.,Jurgensen, C.H.,Long, S.T.,McFadyen, R.B.,Miller, A.B.,Miller, L.R.,Payne, J.A.,Ray, J.A.,Samano, V.,Shewchuk, L.M.,Tavares, F.X.,Wells-Knecht, K.J.,Willard, D.H.,Wright, L.L.,Zhou, H.Q.
Revision History (Full details and data files)
- Version 1.0: 2005-07-19
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2024-11-13
Changes: Structure summary
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